March 14, 2018, 07:45:00 AM

Hi there,

I am trying to process some ion-mobility data that I have acquired on a short gradient.

With the Centwave method, no chromatographic peaks are detected.

With Masspec wavelet, I have this error message:Error: stop worker failed: 'clear_cluster' receive data failed: reached elapsed time limitI first thought it would be a memory problem from my computer but I have check that and it's all right, I have even added more RAM in case.

By consequence, I think it might be coming either from the IMS dimension of the dataset or from the short gradient that I am using.

Anyone would have any experience with XCMS to process IMS dataset, please? Or with a short gradient?

How did you convert the files? Do they show something sensible in for example MzMine?You might want to strip the IMS data. I have no experience with this but if you are converting with msconvert the scanEvent filter might be what you need.With Waters files I have also had good luck simpy deleting the IMS data file (the masswolf converter I was using would crash otherwise)...

A short gradient should make no difference as long as there is still a sensible number of scans per peak.

Hi Jan,Many thanks for your answer! I am glad to know that the short gradient should not induce any difference.I have converted my raw files using Proteowizard using this command:inputCmd <- c()for (filePath in targetFiles){ inputCmd <- c(inputCmd, paste('msconvert.exe', filePath, '-o', saveFolder, '--zlib --filter "scanEvent 1"', sep=' '))}The conversion seemed to be ok, I can open the spectra into MzMine and it seems fine. The problem appears during the peak picking step. Do you think that if I remove the IMS files into the raw folder of the samples (so by deleting the .cdt and .ind files right?), and reconvert them and re-try the peak picking afterwards, it might solve the problem? Many thanks for your help, I really appreciate it!Marine

1) The number of scans per peak is small but enough I think (about 5 to 10 on average, the minimum for a well-defined peak is 7 right?).2) Unfortunately, I have just realised that this dataset I have been acquired in continuum mode and not centroid. So I am assuming that's where the problem is coming from? Sorry, it might be really basic understanding but I am still at the beginning of the learning curve.3) I have adapted the parameters to the dataset and playing with them quite a lot, but it might be coming from here too.